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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs759517314

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:2538744 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000019 (5/264690, TOPMED)
T=0.000104 (24/231388, GnomAD_exome)
T=0.000057 (8/140292, GnomAD) (+ 6 more)
T=0.000171 (19/110854, ExAC)
T=0.00005 (1/18520, ALFA)
T=0.0002 (1/4480, Estonian)
T=0.0000 (0/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.003 (2/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRAT1 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18520 C=0.99995 T=0.00005
European Sub 14152 C=0.99993 T=0.00007
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 504 C=1.000 T=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999981 T=0.000019
gnomAD - Exomes Global Study-wide 231388 C=0.999896 T=0.000104
gnomAD - Exomes European Sub 118930 C=0.999807 T=0.000193
gnomAD - Exomes Asian Sub 48118 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34316 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 14378 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9784 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5862 C=0.9998 T=0.0002
gnomAD - Genomes Global Study-wide 140292 C=0.999943 T=0.000057
gnomAD - Genomes European Sub 75962 C=0.99989 T=0.00011
gnomAD - Genomes African Sub 42056 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13666 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 110854 C=0.999829 T=0.000171
ExAC Europe Sub 66398 C=0.99971 T=0.00029
ExAC Asian Sub 24382 C=1.00000 T=0.00000
ExAC American Sub 11236 C=1.00000 T=0.00000
ExAC African Sub 8036 C=1.0000 T=0.0000
ExAC Other Sub 802 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 18520 C=0.99995 T=0.00005
Allele Frequency Aggregator European Sub 14152 C=0.99993 T=0.00007
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 504 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.0000 T=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
Northern Sweden ACPOP Study-wide 600 C=0.997 T=0.003
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 7 NC_000007.14:g.2538744C>T
GRCh37.p13 chr 7 NC_000007.13:g.2578378C>T
BRAT1 RefSeqGene NG_032167.1:g.22015G>A
Gene: BRAT1, BRCA1 associated ATM activator 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BRAT1 transcript variant 2 NM_152743.4:c.1791G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform 2 NP_689956.2:p.Leu597= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant 1 NM_001350626.2:c.1971G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform 1 NP_001337555.1:p.Leu657= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant 3 NM_001350627.2:c.1266G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform 3 NP_001337556.1:p.Leu422= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant 4 NR_146879.2:n.1974G>A N/A Non Coding Transcript Variant
BRAT1 transcript variant X14 XM_047420034.1:c. N/A Genic Downstream Transcript Variant
BRAT1 transcript variant X15 XM_047420035.1:c. N/A Genic Downstream Transcript Variant
BRAT1 transcript variant X16 XM_047420036.1:c. N/A Genic Downstream Transcript Variant
BRAT1 transcript variant X1 XM_011515177.3:c.2055G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X1 XP_011513479.1:p.Leu685= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X2 XM_011515178.2:c.2055G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X1 XP_011513480.1:p.Leu685= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X3 XM_011515179.3:c.2052G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X2 XP_011513481.1:p.Leu684= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X4 XM_047420028.1:c.1968G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X3 XP_047275984.1:p.Leu656= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X5 XM_011515181.3:c.1875G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X4 XP_011513483.1:p.Leu625= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X6 XM_017011834.2:c.1788G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X5 XP_016867323.1:p.Leu596= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X7 XM_011515184.4:c.1530G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X6 XP_011513486.1:p.Leu510= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X8 XM_047420030.1:c.1530G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X6 XP_047275986.1:p.Leu510= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X9 XM_047420031.1:c.1266G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X7 XP_047275987.1:p.Leu422= L (Leu) > L (Leu) Synonymous Variant
BRAT1 transcript variant X10 XM_011515186.3:c.1702G>A A [GCA] > T [ACA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X8 XP_011513488.1:p.Ala568Thr A (Ala) > T (Thr) Missense Variant
BRAT1 transcript variant X11 XM_047420032.1:c.1699G>A A [GCA] > T [ACA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X9 XP_047275988.1:p.Ala567Thr A (Ala) > T (Thr) Missense Variant
BRAT1 transcript variant X12 XM_017011836.3:c.1618G>A A [GCA] > T [ACA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X10 XP_016867325.1:p.Ala540Thr A (Ala) > T (Thr) Missense Variant
BRAT1 transcript variant X13 XM_047420033.1:c.1615G>A A [GCA] > T [ACA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X11 XP_047275989.1:p.Ala539Thr A (Ala) > T (Thr) Missense Variant
BRAT1 transcript variant X17 XM_024446682.2:c.627G>A L [CTG] > L [CTA] Coding Sequence Variant
BRCA1-associated ATM activator 1 isoform X15 XP_024302450.1:p.Leu209= L (Leu) > L (Leu) Synonymous Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 522955 )
ClinVar Accession Disease Names Clinical Significance
RCV000650123.4 not provided Likely-Benign
RCV001417054.4 Neonatal-onset encephalopathy with rigidity and seizures Likely-Benign
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T
GRCh38.p14 chr 7 NC_000007.14:g.2538744= NC_000007.14:g.2538744C>T
GRCh37.p13 chr 7 NC_000007.13:g.2578378= NC_000007.13:g.2578378C>T
BRAT1 RefSeqGene NG_032167.1:g.22015= NG_032167.1:g.22015G>A
BRAT1 transcript variant 2 NM_152743.4:c.1791= NM_152743.4:c.1791G>A
BRAT1 transcript variant 2 NM_152743.3:c.1791= NM_152743.3:c.1791G>A
BRAT1 transcript variant 1 NM_001350626.2:c.1971= NM_001350626.2:c.1971G>A
BRAT1 transcript variant 1 NM_001350626.1:c.1971= NM_001350626.1:c.1971G>A
BRAT1 transcript variant 4 NR_146879.2:n.1974= NR_146879.2:n.1974G>A
BRAT1 transcript variant 4 NR_146879.1:n.2208= NR_146879.1:n.2208G>A
BRAT1 transcript variant 3 NM_001350627.2:c.1266= NM_001350627.2:c.1266G>A
BRAT1 transcript variant 3 NM_001350627.1:c.1266= NM_001350627.1:c.1266G>A
BRAT1 transcript variant X7 XM_011515184.4:c.1530= XM_011515184.4:c.1530G>A
BRAT1 transcript variant X8 XM_011515184.3:c.1530= XM_011515184.3:c.1530G>A
BRAT1 transcript variant X9 XM_011515184.2:c.1530= XM_011515184.2:c.1530G>A
BRAT1 transcript variant X9 XM_011515184.1:c.1530= XM_011515184.1:c.1530G>A
BRAT1 transcript variant X1 XM_011515177.3:c.2055= XM_011515177.3:c.2055G>A
BRAT1 transcript variant X7 XM_011515177.2:c.2055= XM_011515177.2:c.2055G>A
BRAT1 transcript variant X1 XM_011515177.1:c.2055= XM_011515177.1:c.2055G>A
BRAT1 transcript variant X3 XM_011515179.3:c.2052= XM_011515179.3:c.2052G>A
BRAT1 transcript variant X3 XM_011515179.2:c.2052= XM_011515179.2:c.2052G>A
BRAT1 transcript variant X3 XM_011515179.1:c.2052= XM_011515179.1:c.2052G>A
BRAT1 transcript variant X5 XM_011515181.3:c.1875= XM_011515181.3:c.1875G>A
BRAT1 transcript variant X5 XM_011515181.2:c.1875= XM_011515181.2:c.1875G>A
BRAT1 transcript variant X6 XM_011515181.1:c.1875= XM_011515181.1:c.1875G>A
BRAT1 transcript variant X10 XM_011515186.3:c.1702= XM_011515186.3:c.1702G>A
BRAT1 transcript variant X10 XM_011515186.2:c.1702= XM_011515186.2:c.1702G>A
BRAT1 transcript variant X11 XM_011515186.1:c.1702= XM_011515186.1:c.1702G>A
BRAT1 transcript variant X12 XM_017011836.3:c.1618= XM_017011836.3:c.1618G>A
BRAT1 transcript variant X11 XM_017011836.2:c.1618= XM_017011836.2:c.1618G>A
BRAT1 transcript variant X13 XM_017011836.1:c.1618= XM_017011836.1:c.1618G>A
BRAT1 transcript variant X2 XM_011515178.2:c.2055= XM_011515178.2:c.2055G>A
BRAT1 transcript variant X1 XM_011515178.1:c.2055= XM_011515178.1:c.2055G>A
BRAT1 transcript variant X6 XM_017011834.2:c.1788= XM_017011834.2:c.1788G>A
BRAT1 transcript variant X6 XM_017011834.1:c.1788= XM_017011834.1:c.1788G>A
BRAT1 transcript variant X17 XM_024446682.2:c.627= XM_024446682.2:c.627G>A
BRAT1 transcript variant X12 XM_024446682.1:c.627= XM_024446682.1:c.627G>A
BRAT1 transcript variant X4 XM_047420028.1:c.1968= XM_047420028.1:c.1968G>A
BRAT1 transcript variant X8 XM_047420030.1:c.1530= XM_047420030.1:c.1530G>A
BRAT1 transcript variant X11 XM_047420032.1:c.1699= XM_047420032.1:c.1699G>A
BRAT1 transcript variant X9 XM_047420031.1:c.1266= XM_047420031.1:c.1266G>A
BRAT1 transcript variant X13 XM_047420033.1:c.1615= XM_047420033.1:c.1615G>A
BRCA1-associated ATM activator 1 isoform 2 NP_689956.2:p.Leu597= NP_689956.2:p.Leu597=
BRCA1-associated ATM activator 1 isoform 1 NP_001337555.1:p.Leu657= NP_001337555.1:p.Leu657=
BRCA1-associated ATM activator 1 isoform 3 NP_001337556.1:p.Leu422= NP_001337556.1:p.Leu422=
BRCA1-associated ATM activator 1 isoform X6 XP_011513486.1:p.Leu510= XP_011513486.1:p.Leu510=
BRCA1-associated ATM activator 1 isoform X1 XP_011513479.1:p.Leu685= XP_011513479.1:p.Leu685=
BRCA1-associated ATM activator 1 isoform X2 XP_011513481.1:p.Leu684= XP_011513481.1:p.Leu684=
BRCA1-associated ATM activator 1 isoform X4 XP_011513483.1:p.Leu625= XP_011513483.1:p.Leu625=
BRCA1-associated ATM activator 1 isoform X8 XP_011513488.1:p.Ala568= XP_011513488.1:p.Ala568Thr
BRCA1-associated ATM activator 1 isoform X10 XP_016867325.1:p.Ala540= XP_016867325.1:p.Ala540Thr
BRCA1-associated ATM activator 1 isoform X1 XP_011513480.1:p.Leu685= XP_011513480.1:p.Leu685=
BRCA1-associated ATM activator 1 isoform X5 XP_016867323.1:p.Leu596= XP_016867323.1:p.Leu596=
BRCA1-associated ATM activator 1 isoform X15 XP_024302450.1:p.Leu209= XP_024302450.1:p.Leu209=
BRCA1-associated ATM activator 1 isoform X3 XP_047275984.1:p.Leu656= XP_047275984.1:p.Leu656=
BRCA1-associated ATM activator 1 isoform X6 XP_047275986.1:p.Leu510= XP_047275986.1:p.Leu510=
BRCA1-associated ATM activator 1 isoform X9 XP_047275988.1:p.Ala567= XP_047275988.1:p.Ala567Thr
BRCA1-associated ATM activator 1 isoform X7 XP_047275987.1:p.Leu422= XP_047275987.1:p.Leu422=
BRCA1-associated ATM activator 1 isoform X11 XP_047275989.1:p.Ala539= XP_047275989.1:p.Ala539Thr
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

11 SubSNP, 9 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1617388297 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1660382330 Apr 01, 2015 (144)
3 EVA_EXAC ss1688615629 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2291054417 Dec 20, 2016 (150)
5 GNOMAD ss2736245704 Nov 08, 2017 (151)
6 GNOMAD ss2747761807 Nov 08, 2017 (151)
7 GNOMAD ss2848760602 Nov 08, 2017 (151)
8 SWEGEN ss3000478464 Nov 08, 2017 (151)
9 EGCUT_WGS ss3668409589 Jul 13, 2019 (153)
10 ACPOP ss3734275357 Jul 13, 2019 (153)
11 TOPMED ss4732629282 Apr 26, 2021 (155)
12 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 2578378 Oct 12, 2018 (152)
13 Genetic variation in the Estonian population NC_000007.13 - 2578378 Oct 12, 2018 (152)
14 ExAC NC_000007.13 - 2578378 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000007.14 - 2538744 Apr 26, 2021 (155)
16 gnomAD - Exomes NC_000007.13 - 2578378 Jul 13, 2019 (153)
17 Northern Sweden NC_000007.13 - 2578378 Jul 13, 2019 (153)
18 TopMed NC_000007.14 - 2538744 Apr 26, 2021 (155)
19 UK 10K study - Twins NC_000007.13 - 2578378 Oct 12, 2018 (152)
20 ALFA NC_000007.14 - 2538744 Apr 26, 2021 (155)
21 ClinVar RCV000650123.4 Oct 14, 2022 (156)
22 ClinVar RCV001417054.4 Oct 14, 2022 (156)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
19787586, 14147837, 8671981, 5402718, 7560222, 19787586, ss1617388297, ss1660382330, ss1688615629, ss2736245704, ss2747761807, ss2848760602, ss3000478464, ss3668409589, ss3734275357 NC_000007.13:2578377:C:T NC_000007.14:2538743:C:T (self)
RCV000650123.4, RCV001417054.4, 250359181, 570006841, 10845149777, ss2291054417, ss4732629282 NC_000007.14:2538743:C:T NC_000007.14:2538743:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs759517314

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07